1 Overview

Data

Normalization

Model options

Network processing

cor/cov method: pearson

2 Load and normalize data

Data

Normalization

2.1 Load TCGA data

See prepare.tcga.survival.data function for how to configure parameters.

This uses data packages from obtained from ‘github:averissimo/tcga’ that contain FPKM expression levels.

prepare.tcga.survival.data('brca.data.2018.09.13',
                           'primary.solid.tumor',
                            normalization        = 'center',
                            log2.pre.normalize   = TRUE,
                            handle.duplicates    = 'keep_first',
                            coding.genes         = TRUE,
                            subtract.surv.column = '')

2.1.1 Summary of data

## [INFO]        Loaded data from TCGA: brca.data.2018.09.13
## [INFO]               type of tissue: primary.solid.tumor
## [INFO]   observations (individuals): 960 (137 event / 823 censored)
## [INFO]            variables (genes): 19874

2.1.2 Survival curve

2.2 Load degree data

Network processing

  • Degree calculation: string
  • Edge cutoff: 0
  • Unweighted edges

cor/cov method: pearson

  • only applies if network type is correlation/covariance

2.3 Preparing degree vector

  • Normalize degree between 0 and 1
  • Hub: heuristic( 1 - degree )
  • Orphan: heuristic( degree )
  • trans.fun is a double power to scale the values

see ?glmSparseNet::heuristicScale or ?glmSparseNet::hubHeuristic

# see ?glmSparseNet::heuristic.scale
trans.fun <- function(x) {
    heuristicScale(x) + 0.2
}

2.3.1 Genes with degree above 4000

ensembl_gene_id degree external_gene_name
ENSG00000150991 10394 ENSG00000150991
ENSG00000170325 6346 ENSG00000170325
ENSG00000100300 5797 ENSG00000100300
ENSG00000174775 5614 ENSG00000174775
ENSG00000142208 5573 ENSG00000142208
ENSG00000111640 5363 ENSG00000111640
ENSG00000163631 5260 ENSG00000163631
ENSG00000177606 4952 ENSG00000177606
ENSG00000141510 4936 ENSG00000141510
ENSG00000197122 4903 ENSG00000197122
ENSG00000254647 4592 ENSG00000254647
ENSG00000112062 4187 ENSG00000112062
ENSG00000170315 4114 ENSG00000170315
ENSG00000170345 4010 ENSG00000170345

2.3.2 Original degree frequency

Original

LOG10 Scale on X-axis

3 Model Inference

3.1 Train and test sets

## [INFO] Size of sets: (size/events)
##  * Train: 80.00% ::  767 /  109
##  *  Test: 20.00% ::  193 /  28
## [INFO] Number of variables per model:
Model BaseModel Alpha TargetVars nvars
Elastic Net Elastic Net 0.20 39 42
Hub Elastic Net 0.20 39 40
Orphan Elastic Net 0.20 39 44
Elastic Net Hub 0.20 56 61
Hub Hub 0.20 56 56
Orphan Hub 0.20 56 56
Elastic Net Orphan 0.20 42 42
Hub Orphan 0.20 42 43
Orphan Orphan 0.20 42 44 
## [INFO] note, selected variables could be slightly different from target, to have more accuracy increase nlambda in code

4 Results

4.1 Relative risk distribution

Calculated using the inferred models and the train/test datasets. The higher the better.

Test Set

Train Set

4.2 Kaplan-Meier Curves

4.2.1 Models on test sets

Elastic Net (base model: Elastic Net)

Test set

Training set

Hub (base model: Elastic Net)

Test set

Training set

Orphan (base model: Elastic Net)

Test set

Training set

Elastic Net (base model: Hub)

Test set

Training set

Hub (base model: Hub)

Test set

Training set

Orphan (base model: Hub)

Test set

Training set

Elastic Net (base model: Orphan)

Test set

Training set

Hub (base model: Orphan)

Test set

Training set

Orphan (base model: Orphan)

Test set

Training set

4.3 Summary Table

weighted penalization project tissue cutoff coding.genes alpha model nvars km.train km.test c.index.train c.index.test
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Elastic Net 42 0 0.9662943 0.7971044 0.5039722
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Hub 40 0 0.6129730 0.7768119 0.5014896
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Orphan 44 0 0.0772603 0.7989650 0.5541212
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Elastic Net 61 0 0.8186616 0.8208565 0.5029791
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Hub 56 0 0.2957594 0.8025700 0.5168818
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Orphan 56 0 0.1326391 0.8269326 0.5705065
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Elastic Net 42 0 0.9662943 0.7971044 0.5039722
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Hub 43 0 0.4280535 0.7813763 0.5064548
FALSE string brca.data.2018.09.13 primary.solid.tumor 0 TRUE 0.20 Orphan 44 0 0.0772603 0.7989650 0.5541212

4.4 Non-zero genes

4.4.1 Venn Diagram of selected genes

4.4.1.1 Overlap between models (with same target number of variables)

Base model: Elastic Net with Target Vars: 39 and Alpha: 0.20

Base model: Hub with Target Vars: 56 and Alpha: 0.20

Base model: Orphan with Target Vars: 42 and Alpha: 0.20

Table of genes in models

(not running at the moment)

5 5000 Runs

5.1 C-Index distribution

Test set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Test set) Hub Elastic Net 39 0.20 0.580 0.061 0.580 0.356
C-Index (Test set) Hub Hub 56 0.20 0.598 0.060 0.599 0.377
C-Index (Test set) Hub Orphan 42 0.20 0.584 0.061 0.584 0.358
C-Index (Test set) Elastic Net Elastic Net 39 0.20 0.549 0.064 0.550 0.325
C-Index (Test set) Elastic Net Hub 56 0.20 0.564 0.063 0.565 0.34
C-Index (Test set) Elastic Net Orphan 42 0.20 0.552 0.063 0.552 0.325
C-Index (Test set) Orphan Elastic Net 39 0.20 0.560 0.062 0.561 0.327
C-Index (Test set) Orphan Hub 56 0.20 0.574 0.062 0.575 0.344
C-Index (Test set) Orphan Orphan 42 0.20 0.563 0.062 0.564 0.337
Log-rank (Test set) Hub Elastic Net 39 0.20 0.299 0.284 0.199 4.15e-06
Log-rank (Test set) Hub Hub 56 0.20 0.248 0.265 0.141 2.02e-06
Log-rank (Test set) Hub Orphan 42 0.20 0.287 0.279 0.182 5.26e-06
Log-rank (Test set) Elastic Net Elastic Net 39 0.20 0.385 0.297 0.319 9.78e-06
Log-rank (Test set) Elastic Net Hub 56 0.20 0.351 0.292 0.276 1.72e-05
Log-rank (Test set) Elastic Net Orphan 42 0.20 0.379 0.297 0.312 9.42e-06
Log-rank (Test set) Orphan Elastic Net 39 0.20 0.364 0.290 0.297 1.36e-06
Log-rank (Test set) Orphan Hub 56 0.20 0.332 0.286 0.250 6.47e-06
Log-rank (Test set) Orphan Orphan 42 0.20 0.358 0.290 0.291 1.27e-06

C-Index Distribution

Rank

Elastic Net vs Hub
base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.2841928
Hub with target nvars: 56 alpha: 0.20 0.3134625
Orphan with target nvars: 42 alpha: 0.20 0.2907192

Elastic Net vs. Orphan
base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.7324494
Hub with target nvars: 56 alpha: 0.20 0.7701956
Orphan with target nvars: 42 alpha: 0.20 0.7412038

Hub vs. Orphan
base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.2411301
Hub with target nvars: 56 alpha: 0.20 0.2623140
Orphan with target nvars: 42 alpha: 0.20 0.2451925

Train set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Train set) Hub Elastic Net 39 0.20 0.767 0.017 0.768 0.7
C-Index (Train set) Hub Hub 56 0.20 0.806 0.014 0.806 0.755
C-Index (Train set) Hub Orphan 42 0.20 0.775 0.016 0.776 0.706
C-Index (Train set) Elastic Net Elastic Net 39 0.20 0.806 0.021 0.807 0.723
C-Index (Train set) Elastic Net Hub 56 0.20 0.836 0.017 0.837 0.768
C-Index (Train set) Elastic Net Orphan 42 0.20 0.812 0.020 0.813 0.73
C-Index (Train set) Orphan Elastic Net 39 0.20 0.805 0.019 0.806 0.734
C-Index (Train set) Orphan Hub 56 0.20 0.834 0.017 0.835 0.758
C-Index (Train set) Orphan Orphan 42 0.20 0.810 0.019 0.811 0.736
Log-rank (Train set) Hub Elastic Net 39 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Hub Hub 56 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Hub Orphan 42 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Elastic Net 39 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Hub 56 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Orphan 42 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Elastic Net 39 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Hub 56 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Orphan 42 0.20 0.000 0.000 0.000 0

C-Index Distribution

C-Index Rank

5.2 Log-rank test on Kaplan-Meier models

5.2.1 Log-Rank distribution

Cumulative

Distribution of Log-rank test with groups separated by high and low risk groups

Distribution

Distribution of Log-rank test with groups separated by high and low risk groups

5.2.2 Log-Rank Rank

5.2.2.1 Elastic Net vs Hub

base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.0499714
Hub with target nvars: 56 alpha: 0.20 0.0653053
Orphan with target nvars: 42 alpha: 0.20 0.0571560

5.2.2.2 Elastic Net vs. Orphan

base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.2351056
Hub with target nvars: 56 alpha: 0.20 0.2878296
Orphan with target nvars: 42 alpha: 0.20 0.2411614

5.2.2.3 Hub vs. Orphan

base.model r.squared
Elastic Net with target nvars: 39 alpha: 0.20 0.0447436
Hub with target nvars: 56 alpha: 0.20 0.0523259
Orphan with target nvars: 42 alpha: 0.20 0.0520578

5.3 Consesus genes

5.3.1 Selected genes over all runs

Bar plots of frequencies

Overlap between variables selected

Base model: Elastic Net with Target Vars: 39 and Alpha: 0.20

Base model: Hub with Target Vars: 56 and Alpha: 0.20

Base model: Orphan with Target Vars: 42 and Alpha: 0.20

5.3.2 Selected genes in significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Bar plots of frequencies

Overlap between variables selected

5.3.2.0.1 Base model Elastic Net with target nvars: 0.20 alpha: 39

5.3.2.0.2 Base model Hub with target nvars: 0.20 alpha: 56

5.3.2.0.3 Base model Orphan with target nvars: 0.20 alpha: 42

5.3.3 Genes in Significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Top consensus 20 genes

Gene Overlap total
FLT3 2 5037
TBP 2 4139
CDK14 2 3827
PRDM10 1 3761
UBD 2 3752
NRAS 2 3745
JAK2 1 3716
WWOX 2 3703
LRP11 2 3691
RBMY1E 2 3650
RAC1 1 3650
CLEC3A 2 3637
UBC 1 3633
MAFA 2 3625
LEF1 2 3586
FAU 1 3550
MAPK11 1 3480
AC117457.1 2 3351
HRAS 1 3298
LCE3C 2 3295

All Genes

FLT3(5037), TBP(4139), CDK14(3827), PRDM10(3761), UBD(3752), NRAS(3745), JAK2(3716), WWOX(3703), LRP11(3691), RBMY1E(3650), RAC1(3650), CLEC3A(3637), UBC(3633), MAFA(3625), LEF1(3586), FAU(3550), MAPK11(3480), AC117457.1(3351), HRAS(3298), LCE3C(3295), KIR2DP1(3212), F2(3212), NOTCH1(3151), TSPO(3143), PRKG2(3092), PIK3CA(3062), VSIG8(3036), HSP90AA1(2928), HNRNPC(2848), RAC3(2829), CTNNB1(2803), UBL4B(2785), NOS1(2779), RPS6KA1(2745), UBL4A(2720), LCE3D(2693), TRIM64(2674), LHFPL3(2673), RAC2(2671), SLITRK3(2662), JUN(2583), GAPDH(2560), ZPBP2(2556), PTCHD4(2534), KAT2B(2495), POTEE(2473), EDA2R(2433), NCOR1P1(2387), ELOA3C(2373), EPB41L4B(2357), APOOL(2319), MAPK12(2269), FEZF2(2261), EXD1(2259), LRRFIP2(2248), SLC16A2(2180), HSPA2(2161), SERPINA1(2153), REM2(2122), MAGEB6B(2093), NOS3(2084), ZMAT3(2060), BUB1B-PAK6(2024), MAPK3(2014), SMIM27(2012), PSPC1(1986), ACTL6B(1935), WDFY2(1883), CLRN2(1829), CEL(1822), CD1E(1806), NOS2(1742), TP53(1703), ABCB5(1692), CXorf49B(1663), ELP6(1631), SMIM24(1620), YWHAB(1615), ACTC1(1506), PTCHD4(1501), SPANXD(1451), STBD1(1446), DNAH8(1432), PCDHGA2(1424), DEFB130A(1417), SKOR2(1407), KCNMB2(1395), AKT1(1394), APOH(1389), SRC(1370), YES1(1368), LRRC14B(1334), OR2T5(1318), PELO(1312), L1CAM(1311), ALB(1286), DEFB106B(1282), HSPA8(1282), WT1(1277), CD8A(1273), NFKBIA(1268), PRKN(1268), CPLX3(1263), RHOA(1262), SEMA3B(1260), SIAH2(1249), SPRR2G(1247), ERICH4(1216), FGFR1(1195), USP17L17(1157), DNAAF4(1132), CPLX2(1115), DMC1(1095), TBPL2(1086), RIOX1(1081), TYRO3(1064), SLITRK3(1039), CD8A(1039), FAM71A(1030), CLEC4G(1023), KCNK3(1021), AMBN(1017), PRAMEF17(1017), GUCY2D(1012), XKR7(998), OR10P1(997), KLHDC7B(996), PYY3(994), TMEM31(986), PLA2G1B(951), FOXD1(939), ACTG2(929), AL355987.3(922), PRAMEF19(917), AL049844.3(904), PSME2(886), PGK1(867), FOS(867), CCDC97(858), IL13RA2(856), GON7(842), RPH3A(839), SRRM5(837), CD99L2(833), TUBB4A(820), OAS1(786), C1orf226(785), MAPK1(782), SPRR4(776), TCP1(775), FO681492.1(772), KRAS(767), OPN4(763), C2CD2(753), EGFR(752), INPP5A(740), GREB1L(740), XG(721), SPATA31E1(717), CR1L(717), IMPDH2(716), CLEC4M(710), MAPK14(709), FIBCD1(705), CIB4(686), UBB(680), IGF1R(666), FOXJ1(655), BCL2(655), SERINC4(654), IMPDH2(651), SUN3(645), IL27RA(643), TCL6(632), FGFR3(623), SSX7(619), PAK6(618), BRD4(617), ZBED6CL(615), PCSK1(612), CDK1(610), SPPL2C(599), MAGEB4(589), C1orf53(581), CCDC83(574), RPL5(573), ENSG00000281028(572), SH3BP1(571), GDPGP1(570), OPN4(569), CDKN1A(565), PCSK1(565), RANBP2(563), CAT(558), HDGFL1(557), NFKBIE(552), CDC42(544), ACTA1(542), NGB(534), CPEB1(533), DDAH1(526), ACTL8(520), ACTA2(509), SPP2(508), LRRC8D(502), PCDHA1(499), TUBA3D(498), ABCG4(492), SMARCA2(487), SPIB(481), LHX5(476), SHISAL2A(473), XRCC1(471), EPHA3(470), CCDC187(468), TRIM67(462), ESRRG(456), TEKT2(455), TMEM251(445), PDGFRB(442), CD1B(441), RHOU(434), RPL5(431), VWC2(430), CST1(427), IGFBPL1(425), NLRP2(424), LCE3E(419), SIPA1L1(411), C8orf33(401), FLT1(399), USP17L17(399), ADGRL3(398), STXBP5(396), C11orf95(393), QRFPR(390), SNAPC2(388), RHOH(387), DSCAML1(386), PCMT1(385), LINC00115(384), CCSER1(383), TMEM120B(381), WT1(378), CXCL13(376), APOA5(374), TOP2A(373), RABL2A(370), TMEM69(356), RAPGEFL1(353), IL18(353), EPHA3(346), ATP8A2(344), HYAL3(335), ADGRG6(333), ERP27(332), CLIC6(332), PCMT1(330), NFKB1(329), RAP1GAP2(328), TOR1B(328), GSTM4(324), IFNG(317), TBPL2(317), TUNAR(313), EHMT2(312), RTL8B(303), APOBEC3D(297), DECR1(285), NXNL2(284), FUZ(283), ARMC12(282), GPR152(282), SHISAL1(277), AC069503.2(275), SNW1(274), IWS1(269), RELB(266), RIPK4(266), CHTF8(264), MORN3(261), DEF6(260), REM1(259), KDR(259), HDAC3(258), KLRC1(253), PROSER2(250), ZBED2(248), ACBD5(247), SFMBT1(246), RPL14(246), TGFB1(245), LRRC37A6P(243), MAP3K3(242), SLC35G2(238), HYAL1(235), ROPN1L(233), KRTAP1-4(228), H2BU1(227), RPS18(227), YWHAH(220), PTPN23(217), PCDHGB5(217), PIRT(212), MGAM(210), DPEP2NB(209), CCL1(209), RUNX1(208), UMPS(207), SSTR1(206), GNA11(205), CST7(198), C17orf99(195), YBEY(192), LTA4H(190), PRR20A(188), NMNAT2(185), CASP7(185), CD24(184), DAXX(184), PIGF(182), RBBP8(182), VGF(181), CXorf56(179), PCYT1A(178), CASP7(177), RDH11(177), DEFB104B(175), TMEM233(175), PPIB(174), MYC(173), OSGEP(171), ZDHHC9(170), GPR142(169), IRF2(167), RAD51B(167), PTEN(163), C1orf127(162), XKR3(157), ACTR8(156), KLRB1(154), LDLRAD3(154), CABCOCO1(154), LYRM7(153), GSTZ1(153), BTN2A2(151), UNC79(151), MAP2K6(148), TH(147), ZSCAN21(145), MMGT1(145), YBEY(144), PAX7(144), NEDD8(143), POTEI(142), GTF2B(140), GSTZ1(139), MAP6D1(139), NFE2(138), CLNK(137), NPR3(136), CDK4(136), EXOC3-AS1(134), HSPA1A(132), PAX7(131), TAPBPL(131), KLRB1(131), DNAJB5(131), HSPA9(130), MCM5(128), CDK6(128), QARS1(128), CDK16(127), BIRC3(125), ADCY3(125), LCK(125), AL355916.3(125), GPR107(124), KCNH6(124), QPRT(123), PCDHB3(122), SCG2(121), C2orf15(121), TIE1(120), PLEKHH1(119), STX7(119), INSR(119), HDAC1(118), ZFAND4(116), ZNF75D(116), CDK2(115), PRECSIT(114), ING2(114), MGAM(114), C3orf62(113), CPT1A(113), HES5(113), SLC18A1(112), EFCAB12(112), FOXR2(112), EPHA5(111), ARMH1(110), ISG15(110), MAP2K6(109), C6(108), BSND(108), CTSF(108), NDUFB1(108), FAM47E-STBD1(105), BMP7(104), ARMC1(104), DCUN1D4(104), FGF2(102), TMEM155(102), CADM4(101), RND2(99), ENPEP(99), QARS1(98), AK7(98), IDNK(97), IKZF3(97), RAP1A(97), CREB1(97), GFI1(97), ACTL10(97), CACNA1H(96), CFHR1(96), TOP2B(95), ELAVL1(94), GNA11(93), C16orf71(93), SLC20A2(93), PLEKHA8P1(92), FYB2(92), PCDHGA11(92), RSPH1(92), BEND5(90), GCSAM(89), EMC2(88), MATK(88), C7orf77(87), SLC1A4(87), GALNT9(86), EIF5AL1(86), PARP3(86), LACTB2(86), TPMT(85), CD1A(84), B4GALT1(82), DISP2(82), SEPTIN12(81), LST1(81), KRTCAP3(80), CCL5(80), CCNA1(79), HHIPL2(79), PLG(79), TNF(79), SLA(77), UGT2B4(77), GBP2(76), EN2(76), CDHR4(76), RAB2A(75), CACNG3(74), PRAMEF11(74), LINC02694(73), Z98752.3(73), OAS3(73), TMEM14B(72), CA2(72), IL6(72), NEUROG2(72), OR5K2(72), CCL5(71), LYPD4(71), VSIG1(70), TTLL5(70), CD163L1(69), EN2(69), RSKR(69), PRPF38B(68), CFAP57(68), ARG2(68), SEC14L2(67), OTUD3(67), RGL3(67), HDAC9(67), OAS2(67), ANKRD63(67), OR2I1P(67), PRSS2(66), UGDH(66), CCDC28B(65), C1QTNF7(65), SURF4(65), SCRT1(65), HINT3(64), UNC50(64), FOXF1(64), SKP1(64), GTPBP1(63), RASL11B(63), EPHB6(62), SMR3B(62), MYD88(62), PCSK4(62), AIMP1(62), TBC1D3E(62), YIPF4(61), TMEM156(61), DEFB104B(61), LYPD4(61), TAFA4(60), AGBL2(60), TTC39C(60), CYTL1(60), AL391650.1(60), RALA(60), RHOJ(60), JAK1(60), CHEK2(60), BAMBI(59), POLR2C(59), SVOPL(59), MTOR(59), SDHC(58), ZRSR2(58), PTGES3(58), APOL2(57), AFG1L(57), CCDC81(57), GPR171(57), STARD3NL(56), TBPL1(56), CRISP3(56), C1orf194(56), SPRR2B(56), MBLAC1(55), EPHA5(55), NAT16(54), KYAT3(54), ITGA2(54), JRKL(53), RAD51D(53), PIM2(52), RGS3(51), PDE4C(50), OR2I1P(50), SLC1A1(50), USP41(50), EPHB4(50), SCRN1(49), FYN(49), ADCY10(49), MAPK13(49), CRISP2(48), UBTF(48), TNN(48), FAM155B(48), CDK5(48), TTC16(48), CALB2(48), TIFAB(48), CCDC74B(47), ATF7IP2(47), MRE11(47), QPRT(47), RPL28(47), YWHAG(47), LIMCH1(46), FOXQ1(46), OR5AU1(46), SCUBE2(46), MINDY4B(46), SLC25A43(45), APOBEC3F(45), NKX2-1(45), LPAR4(45), CCDC169-SOHLH2(45), PDE4C(45), STXBP1(45), SCARB2(45), ACLY(44), RGS9(43), GSTT2B(43), CRCT1(43), HLA-DQB2(43), HSCB(43), AC090360.1(42), ISY1-RAB43(42), CBLN4(41), MAPKAPK3(41), TOGARAM2(41), IZUMO4(41), PDHA2(41), CCL19(41), NOL4(40), CCDC157(40), ISY1-RAB43(40), INSRR(40), TTLL5(40), MECP2(40), ALKBH1(39), CFAP251(39), STAG3(39), LHX9(39), PLXNB1(39), EFCAB12(39), LINC02694(39), TRMT2B(39), PCDH12(38), PRDM12(38), ATPSCKMT(38), WNT3A(38), HMHB1(38), C17orf67(38), PRSS2(38), CFAP299(37), PPIAL4E(37), ADRB1(37), MAPK6(37), MAJIN(37), RXFP1(37), MICU2(36), NDRG1(36), MAPK4(36), RHOC(36), FOXQ1(36), TUBA1A(36), IZUMO4(35), BCAN(35), HNRNPD(35), BATF(35), MAPK7(35), SLC2A4(35), C17orf67(35), PCDHB2(34), SPX(34), MORN2(34), FAM72C(34), SYK(34), Z84492.2(33), FAM72C(33), CABYR(32), MICB(32), FAM24B(32), HSPA5(32), GGT1(32), GSTT2B(32), GART(32), KLF11(32), SLC30A10(32), PLXNB3(32), PLEKHO1(31), ADRB1(31), HNRNPA1(31), SECISBP2L(31), ZNF556(31), GP6(31), KRT32(30), PSEN1(30), TESPA1(30), GASK1A(30), SCGB1C2(30), ENSG00000228439(29), ZNF750(29), RGS1(29), NOVA2(29), MEIOB(28), CCDC51(28), PCDHGA12(28), CAB39L(28), ACSL1(28), KIF5B(28), ZNF556(28), OR8H1(28), AL391650.1(28), SPATC1L(27), PLXNB3(27), RPL19(27), ACTG1(27), ANO3(26), HAUS2(26), RIPK2(26), CSN3(26), Z84492.2(26), FAM184B(25), PAK1(25), BATF(25), CYP4F11(25), AL162231.1(25), PCDHGA1(25), GSTM1(25), ERBB2(25), GNL3(25), RHOBTB3(25), CACNA1H(25), HDAC2(25), TRPC5OS(25), UNKL(24), KRT8P41(24), ANKRD54(24), MCM5(24), KIAA1191(24), RRAS2(24), PSD2(24), ITFG1(23), LRRC23(23), NFKB2(23), EPHA1(23), PDP1(23), CD3D(23), CXCR6(23), CLDN25(23), SEZ6(22), ZFAND1(22), ZNF326(22), C2orf91(22), PRKCZ(22), ABL1(22), CCND1(22), HIF3A(22), LIMD2(22), KIT(22), HMHB1(22), DUSP23(22), ALOX15(22), LIMD2(21), TRAPPC12(21), BEX5(21), CHCHD2P9(21), GATD3B(21), BAG1(21), GLRXP3(21), LCP1(21), ACTR1A(21), THAP8(21), H2AW(21), LIN28B(21), ATP6V1G2-DDX39B(21), NDST4(20), TNFRSF18(20), PCDHA2(20), FKBP5(20), DIRAS3(20), SCG2(20), TMEM225B(20), SOX30(19), NEXMIF(19), ATG4A(19), THAP8(19), FAM131A(19), LHFPL1(19), TMEM200C(19), CTNNA2(19), DNTTIP2(19), PSME1(19), SRF(19), CPLANE2(19), AC020909.1(19), RIBC1(19), BEX5(19), PEG3(19), AC012254.2(19), CCDC74A(18), BTBD6(18), FP565260.1(18), ACAA1(18), GSK3B(18), BLNK(18), RHEB(18), PSKH1(18), DNAAF3(18), TOX(18), ENSG00000274897(17), PLA2G2D(17), CNR1(17), ECHDC3(17), GPA33(17), ZNF589(17), CSKMT(17), CNR1(17), CASP9(17), PCSK6(17), NTRK3(17), CACNG8(17), IVL(17), FAM178B(17), GPR25(17), LKAAEAR1(17), FAM162B(17), TRIQK(17), LINC01036(17), NUB1(16), CS(16), PEX10(16), RIBC1(16), TMEM238L(16), MGLL(16), MYH14(16), SNX3(16), PRLHR(16), ADCYAP1(16), CCDC81(16), AC092143.1(16), HLA-DOB(16), ZP1(15), FAM81B(15), FAM111A(15), NUDT17(15), RAET1G(15), LRRC8A(15), CYP2C9(15), ZNF394(15), HSPA4L(15), MRGPRG(15), POTEKP(15), NAT14(14), SLC39A8(14), NEK10(14), BAALC(14), GP9(14), C2CD4A(14), ENSG00000274897(14), PGR(14), HACE1(14), HUNK(14), FHAD1(14), ACKR3(14), VIP(14), CCDC74B(14), YWHAZ(14), CXXC4(14), AL162231.1(14), IGF2R(14), IGSF9B(13), AMBRA1(13), WDR38(13), THAP9(13), CDK5R2(13), SPDYC(13), PRRT4(13), SPTY2D1OS(13), CD6(13), PNPLA6(13), IGFALS(13), RHBDL1(13), ACTRT1(13), PDE6B(13), DERL1(13), BCL2A1(13), IQSEC1(13), ZNF449(13), GRB2(13), HTR1D(13), C1orf194(13), RGS9BP(13), MRTFA(13), ZBED1(13), LHX1(13), GATD3B(13), REC8(12), NTSR1(12), TMOD2(12), MCOLN2(12), PSKH1(12), TPCN1(12), TUBGCP5(12), NUB1(12), FGFR2(12), ACACB(12), CREM(12), GSK3A(12), BCHE(12), CALML4(12), USP26(12), SCRN1(12), WT1-AS(12), TTC32(12), C5orf60(12), C6orf226(12), LTB(12), PRR20E(12), JRK(12), TUBA4B(12), RBM15B(12), PCDHB16(12), TUBGCP5(12), TMEM98(11), ERF(11), CYTIP(11), NEU2(11), SSX2IP(11), STRA6(11), CAMK4(11), CYP2S1(11), L34079.1(11), SH2D2A(11), MED17(11), ALKBH1(11), APEX1(11), GHRHR(11), GABRA4(11), OCRL(11), NGDN(11), NDST4(11), IL21(11), GPA33(11), HSP90B1(11), NSG2(11), PDE3A(11), TIGIT(11), C6orf120(11), NPIPB9(11), MYL4(11), TMEM200C(11), ZNF321P(11), KLRC4-KLRK1(11), URB1-AS1(11), AC091167.6(11), Z83844.1(10), BAG1(10), SAP130(10), SDHAF3(10), ZNF705G(10), HEBP2(10), IGSF9B(10), MCOLN1(10), HSD17B7P2(10), YY1(10), PPP2CB(10), AMH(10), MET(10), TMEM245(10), AMBRA1(10), FAM120B(10), APC2(10), CDK18(10), GPR42(10), SLC4A10(10), SCN3A(10), TDRD10(10), SUN1(10), ADRA1B(10), FRG2C(10), ROBO2(10), TOGARAM2(10), PRMT6(10), C2orf72(10), COG8(10), PRRT4(10), H2AL1RP(10), CDK11B(10), EML2-AS1(10), IL12B(9), CFAP94(9), RTL8C(9), TRPV3(9), CTSW(9), APOM(9), RBM15B(9), DGAT2(9), CS(9), ACTB(9), TYK2(9), TP53I3(9), FAM199X(9), MEA1(9), PNKD(9), RHOB(9), TIRAP(9), LRGUK(9), KCNE2(9), TMIGD2(9), ADCY6(9), NUDT17(9), C19orf54(9), TMEM253(9), IFITM10(9), CHMP4A(9), CDH19(8), LAMP3(8), ADGRB2(8), CISD1(8), MED18(8), IGSF11(8), EI24(8), ZNF208(8), ALKAL1(8), KRTAP3-3(8), SFTA3(8), SRD5A2(8), CREBBP(8), ST3GAL1(8), RHOBTB2(8), ERCC1(8), CPS1(8), FOXP3(8), IP6K2(8), CAD(8), ESR1(8), RASD2(8), REC8(8), PARD6A(8), IL12B(8), RND3(8), MEF2D(8), GBP1(8), C20orf85(8), PCK1(8), PCNA(8), GABBR2(8), AIG1(8), GPAT4(8), TAGLN2(8), RPL27A(8), NAB2(8), THAP9(8), CLVS1(8), WDFY3-AS2(8), NAP1L1(8), TAF9B(8), OR7D2(8), UBQLN2(8), CLEC9A(8), LINC01588(8), AL512785.2(8), TSPY1(8), PEX3(7), PHF23(7), PLGRKT(7), SLAIN1(7), ZNF222(7), COX6B2(7), LALBA(7), EMB(7), CTXN1(7), SH3D21(7), XKR9(7), TTC4(7), IGLL5(7), SMIM17(7), MMP25(7), ZNF275(7), TFPI2(7), SLC29A1(7), PASK(7), SUMO1(7), CD207(7), SGK1(7), OASL(7), SDHC(7), CALM2(7), MTA2(7), DIP2C(7), EIF5B(7), MRPS18C(7), F2RL2(7), RET(7), CYP2S1(7), SMIM4(7), CDH2(7), BFSP2(7), LHFPL1(7), PRKG1(7), CHCHD2P9(7), SELL(7), ALKAL1(7), ACCSL(7), KRTAP5-6(7), UBA52(7), USP17L15(7), PPIAL4D(7), THTPA(7), AC087289.3(7), MAGEA9B(7), FAM214B(6), SH2D2A(6), MOSPD1(6), COTL1(6), CCDC9(6), THEM6(6), ST6GALNAC4(6), C1orf94(6), TUBA3E(6), NFIA(6), WDR41(6), MGAT5B(6), PAQR8(6), C12orf66(6), FGD6(6), OOEP(6), GMNC(6), OR2A1(6), AC011479.1(6), SYT1(6), RPS6KA2(6), PRKACA(6), KAT6A(6), MAPRE3(6), CABP7(6), CRHR2(6), ZCCHC17(6), SNX9(6), EMP1(6), RPL11(6), CELSR2(6), C11orf49(6), TUBA3E(6), XRCC4(6), CAMK4(6), FAM81B(6), WNT3A(6), TFF1(6), WDR41(6), STK17A(6), ABCA1(6), MTNR1A(6), CLIC3(6), NLGN1(6), CMTM8(6), SLC23A1(6), CES3(6), FGD6(6), DGAT1(6), NBPF4(6), DTHD1(6), RAET1G(6), TMA7(6), APOBEC3G(6), AC090360.1(6), ZNF587B(6), PRAG1(6), FCGBP(6), LYZL6(6), ARSF(5), FOLR3(5), UPK1B(5), SPINK4(5), GPR45(5), ENDOV(5), HLA-DQA1(5), DCAF12L2(5), TTC25(5), URGCP-MRPS24(5), PLXND1(5), TMEM98(5), HSD17B6(5), ATP6V0A1(5), RPL31(5), LAMP3(5), NAT14(5), EXOC1(5), MMP9(5), NTSR1(5), DMAC2(5), EZH2(5), STX2(5), FRK(5), HHLA2(5), CHMP3(5), AKT3(5), SERPINC1(5), NUP43(5), ADGRB2(5), PDZD2(5), NOTCH2(5), TRIM45(5), HNRNPA1(5), REPS1(5), ANK2(5), MARCHF6(5), YIPF5(5), ANK3(5), ARL11(5), TNFRSF14(5), ADAM9(5), CYP4F11(5), CCDC121(5), RPS6KA3(5), CTXN1(5), TP53TG1(5), NAP1L2(5), TPRG1(5), TMEM221(5), SUMO2(5), KRT40(5), SPINK8(5), GOLGA8N(5), TSPY4(5), IGLL5(5), MMP12(5), TMEM238L(5), GABRQ(5), FP565260.2(5), PLXND1(4), PARP12(4), KAT6A(4), SLC5A5(4), UNC93B1(4), GTF3A(4), TSGA10(4), LMBR1L(4), CCNO(4), FBXO43(4), LBHD1(4), OXR1(4), CCDC103(4), TMC7(4), VPS37D(4), GPR157(4), PGBD4(4), SCFD2(4), PLEKHN1(4), SAXO2(4), WDSUB1(4), DISP3(4), CNEP1R1(4), STRC(4), PARP12(4), DDX43(4), DLG3(4), ZNF416(4), PDE6C(4), TIMM9(4), ZDHHC15(4), TOX3(4), PRKAG2(4), TASOR2(4), UNC93B1(4), PTPN5(4), STC2(4), EEF1B2(4), ERRFI1(4), SFPQ(4), GADD45A(4), RPF1(4), HS3ST2(4), MORF4L2(4), MED18(4), CCNA1(4), DPH6(4), ECHDC3(4), CCNJL(4), P2RX4(4), TSGA10(4), CXCL9(4), PPP3CA(4), SLC39A8(4), FURIN(4), MARVELD3(4), ARFGAP2(4), CC2D1B(4), GBP5(4), LRRC43(4), CCDC116(4), NFIA(4), C1orf189(4), RHO(4), LMBRD2(4), IFI27L1(4), TRPV3(4), TMC7(4), PRKCE(4), ENDOV(4), H2BC4(4), PRR36(4), DDX41(4), NBPF6(4), ERAS(4), CERKL(4), WDSUB1(4), STK39(4), CCDC160(4), TTC25(4), GMNC(4), CXorf49(4), OR2A1(4), NEDD8-MDP1(4), AC010326.2(4), SRD5A2(4), ENSG00000261833(3), HPS4(3), ISYNA1(3), TMEM245(3), IRGC(3), IGFLR1(3), TNFRSF19(3), DPH6(3), MARVELD3(3), POMGNT2(3), ZNF256(3), SDHAF4(3), NCAM2(3), CDK19(3), PDIA3(3), PSCA(3), RPSA(3), MSANTD4(3), GPR132(3), VEPH1(3), FAM114A1(3), ZNF560(3), C11orf98(3), ZMYND10(3), TRAF3IP3(3), CD74(3), GABARAPL2(3), SOX30(3), PHF23(3), XK(3), GINM1(3), DCX(3), MOXD1(3), EPDR1(3), CHGB(3), MFSD11(3), HPS4(3), Z83844.1(3), ABCD1(3), BMF(3), BPNT2(3), HNRNPUL1(3), ISYNA1(3), BLVRA(3), MAP3K8(3), FOLR3(3), CD83(3), GHR(3), RNF7(3), RTN4(3), ADPRS(3), MYB(3), FOXO3(3), NUDCD1(3), HERPUD2(3), MAX(3), LSM8(3), IFT22(3), DLL4(3), SAG(3), SAMD10(3), MORC4(3), EPHB2(3), KLHL36(3), GPR55(3), CCDC115(3), MMP7(3), COPS4(3), CLBA1(3), EVA1B(3), RALB(3), ANO7(3), UGCG(3), CAMK2G(3), PAK1(3), MERTK(3), ZUP1(3), ZNF18(3), MOV10(3), CD1C(3), CCDC24(3), LSS(3), COX6B2(3), TAL1(3), CDC20B(3), SSX3(3), FAM111A(3), MEI1(3), TRIM49(3), MUC15(3), CST2(3), CCDC106(3), RMDN1(3), PGBD5(3), HLA-DQB1(3), R3HDM2(3), SEPTIN1(3), C11orf54(3), GBP6(3), DOCK8-AS1(3), SDR42E2(3), POLR1D(3), PNRC2(3), SERPINA3(3), SDHAF3(3), ELOVL2(3), TMEM229B(3), HOXC4(3), OOEP(3), LRRC73(3), PSMB8(3), ERICH2(3), C2orf91(3), DIO2(3), KRT8P41(3), MCTS1(3), PEG10(3), PCDHAC2(3), NAA80(3), AL691442.1(3), SRSF8(3), AC024592.3(3), AC243967.1(3), SMIM17(3), AL591806.2(3), URGCP-MRPS24(3), AL603832.3(3), H4C9(3), ZMYND10(2), ZNF416(2), SIRPG(2), APOL4(2), GABRE(2), FGF8(2), FBXO9(2), SPRYD7(2), GTSF1L(2), TTI2(2), TCN1(2), TMEM60(2), BTBD16(2), B4GALNT3(2), ARHGAP26(2), SUSD3(2), DRC1(2), TMEM174(2), ENOX2(2), TMEM130(2), HES3(2), LAMTOR4(2), PLEKHG4(2), CRYBA4(2), SPINK8(2), TAPBP(2), AP000311.1(2), CFTR(2), SARM1(2), FAM214B(2), AKAP8L(2), CCDC88C(2), STMN4(2), SEC63(2), PEX3(2), ARSF(2), GNAI3(2), FRMPD1(2), NSF(2), REXO2(2), AMPH(2), CHMP2B(2), IRAK3(2), RAB18(2), PVALB(2), EP300(2), PLEK2(2), PNN(2), GLA(2), AKT2(2), PLEKHA4(2), PMPCB(2), SPOCK2(2), RPS6KB1(2), MMD(2), COMMD9(2), ATP5F1B(2), IQCG(2), CYTIP(2), VAMP4(2), CFAP94(2), CCDC92(2), SFRP5(2), TRIM25(2), GTSF1L(2), SCGB1D2(2), INSIG2(2), IGFLR1(2), PZP(2), FGD3(2), EPS15L1(2), GAD1(2), THEM6(2), CAMSAP1(2), LANCL2(2), REEP2(2), IRAK2(2), FKBP11(2), TCN1(2), GPR45(2), IL10(2), TLR4(2), GRHPR(2), FGFBP1(2), STRA6(2), SLAIN1(2), GATA6(2), C1orf94(2), ITGA10(2), LYG1(2), POMGNT2(2), SNCA(2), ARHGAP26(2), CNBD2(2), CCDC102B(2), CLGN(2), MCOLN2(2), SDHAF4(2), NCAM2(2), OTUD6B(2), ADK(2), SUSD3(2), CBR1(2), TMEM190(2), MEIOB(2), LBHD1(2), ATF3(2), ACP6(2), DAPL1(2), NEK10(2), ZNF589(2), FABP7(2), OXR1(2), TMEM130(2), PRKCB(2), RRAD(2), C15orf48(2), CCDC103(2), LALBA(2), PSCA(2), TMEM223(2), PCSK9(2), CD52(2), AGPAT2(2), TMEM192(2), PAQR8(2), RSL1D1(2), ZNF274(2), TTC36(2), RASGRP1(2), HES3(2), ZNF25(2), VPS37D(2), C15orf56(2), CALML3(2), ERN1(2), OR4A15(2), UBA7(2), CAMK1D(2), C19orf71(2), ZNF730(2), LRRC55(2), SCFD2(2), ZNF284(2), KRTAP19-2(2), RNF220(2), OR7A5(2), MAGEB16(2), HLA-DRB1(2), CRYBA4(2), HLA-DQA1(2), SPTAN1(2), FAM114A1(2), CNGA1(2), C2CD4A(2), AGPAT1(2), CFAP99(2), LNP1(2), ZNF99(2), HNRNPUL2(2), AP000790.1(2), ACSM4(2), POTEJ(2), GAGE12H(2), PLEKHM1(2), TAPBP(2), MPC1L(2), ZNF722P(2), PSG4(2), OSTCP1(2), CDK3(2), CLDN23(2), AC011479.1(2), L34079.1(2), AC114490.2(2), TBC1D3K(2), TMEM269(2), AC036214.3(2), AC244517.10(2), ENSG00000243444(1), FGR(1), RGPD5(1), OTC(1), FLT4(1), ZIC2(1), RAD51(1), CDK17(1), MPC1(1), RHOBTB1(1), P4HA2(1), TEAD2(1), SCGN(1), OSTM1(1), FAM234B(1), PIR(1), RBBP9(1), RPGRIP1(1), UPRT(1), MYO3A(1), LGALS2(1), APOL4(1), TRIB3(1), OXT(1), NKAP(1), MOSPD1(1), ASB9(1), GABRE(1), RPAP1(1), RHOV(1), POP1(1), UBXN8(1), EPHX3(1), NUMBL(1), MEIS3(1), GRB10(1), CCL24(1), TYRP1(1), B9D1(1), APOC3(1), SLC11A2(1), GLI1(1), PDE10A(1), FAM172A(1), HRH2(1), WNT5A(1), SLC41A3(1), CCT4(1), GBP3(1), SLC19A2(1), MESD(1), BBOF1(1), IFIT2(1), MXI1(1), PPP3CC(1), AKAP1(1), CSTA(1), GTF3A(1), CISD1(1), SPRYD7(1), TUBA1B(1), PLP1(1), DDX27(1), KCNK17(1), BFSP1(1), ST3GAL3(1), SYNGR3(1), SRD5A3(1), HOXD1(1), TTI2(1), DOCK6(1), PRRG1(1), ABCB7(1), ACTR10(1), ZSWIM3(1), ZBED3(1), SFTPD(1), TMTC1(1), GRP(1), BIVM(1), ERCC5(1), ADAMTS8(1), KLB(1), TMEM60(1), MRAP2(1), TAAR5(1), CYP27A1(1), NKX2-1(1), CHAD(1), SAP130(1), KLF4(1), WDR38(1), PIM1(1), CYP1B1(1), PLCE1(1), CIR1(1), HNRNPD(1), NAAA(1), CLSTN3(1), GPR84(1), WDR93(1), BCAS3(1), DYM(1), DPP9(1), TRPM2(1), SIGLEC10(1), WDTC1(1), NECTIN4(1), DUSP10(1), THNSL2(1), GIN1(1), GTF2H2(1), CRIP3(1), IGSF1(1), BIN3(1), HIKESHI(1), MTMR12(1), RABGAP1L(1), ZSCAN1(1), GPR180(1), ANKRD22(1), CIBAR2(1), KLF10(1), OXA1L(1), FAM81A(1), DYRK1A(1), PEX10(1), CCAR2(1), C1R(1), ACE(1), ZNF208(1), LCN1(1), COX7A1(1), SSTR5(1), RPL29(1), LRATD1(1), TIPARP(1), IL17RE(1), PGRMC2(1), ANAPC10(1), CASP3(1), SAP30L(1), FBXO33(1), AKR1E2(1), OXGR1(1), UCMA(1), FAM204A(1), ENOX2(1), PPP1R36(1), VWA2(1), SGPL1(1), MRPL16(1), CABP2(1), MGAT5B(1), GNG4(1), IL7R(1), ACTBL2(1), SIN3A(1), GP9(1), COX7B2(1), IRX2(1), ZNF672(1), CHST11(1), ENC1(1), CTSW(1), COL6A5(1), HSPA6(1), RHOD(1), TRIB1(1), RBM4(1), TMEM81(1), LEP(1), BTC(1), SART1(1), LONRF3(1), TMEM270(1), LRRN1(1), ZNF135(1), FUT2(1), PPFIA3(1), MAGEF1(1), C18orf32(1), DPY19L3(1), FOXE1(1), GAK(1), SNX18(1), TSPYL5(1), OR51E1(1), NPM1(1), FAM89A(1), PGBD4(1), ZNF623(1), GPR132(1), PRR32(1), RP1L1(1), MRGPRX2(1), NUDT14(1), KMT5A(1), EIF3C(1), ACTRT3(1), SH3BGR(1), P4HB(1), MORN5(1), PCYT2(1), CCDC73(1), PLEKHN1(1), NANOS1(1), SAXO2(1), RHCE(1), LRRK2(1), SYCP2(1), SRGAP2B(1), NPIPB15(1), FAM163B(1), ZNF470(1), ADAM32(1), ZNF560(1), HMGN5(1), RPS6KL1(1), DCAF12L2(1), NOS1AP(1), RORB(1), SP5(1), CASP12(1), C6orf47(1), RNF39(1), DISP3(1), LINC01556(1), CNEP1R1(1), ITPRIPL2(1), KLRC2(1), TTLL13P(1), RBMXL1(1), ZNF888(1), SPDYE3(1), RAD51AP2(1), GPR33(1), C16orf90(1), ZNF705G(1), FMO9P(1), C7orf65(1), CENPVL1(1), HNRNPA1P48(1), FAM236D(1), C5orf67(1), SBK3(1), MCIDAS(1), ZNF853(1), KIR3DL2(1), TDGF1(1), PSG11(1), AMY2A(1), SMIM34A(1), TTC4(1), ZCCHC3(1), ARPIN-AP3S2(1), SHANK3(1), INMT-MINDY4(1), AC068775.1(1), AC018523.2(1), AC025165.3(1), C17orf49(1), AC005726.1(1), GH1(1), AC073508.2(1), ANXA8(1), AC007998.2(1), AC069257.3(1), ARL2-SNX15(1), F8A2(1), TBC1D3B(1), CCL4L2(1), CCL3L3(1), FP565260.3(1), CCL3(1), C11orf98(1)

5.4 Best C-index test in all runs

Best Elastic Net model (C-Index test)

[INFO] Coefs. list

[1] “ABCB5, ADGRL3, AMBN, APOH, APOOL, CCL1, CD99L2, CEL, CLEC3A, CLRN2, CPLX3, DEFB106B, ELP6, ESRRG, FEZF2, FLT3, FOXQ1, GUCY2D, H2BU1, HDGFL1, KCNK3, KIR2DP1, LCE3C, LCE3D, LHX5, LRP11, LRRFIP2, MAFA, MAGEB6B, MCOLN1, MECP2, NCOR1P1, NFKBIA, OR10P1, OR2T5, PELO, PRLHR, PSME2, PSPC1, PTCHD4, PYY3, RDH11, RGS3, RPH3A, RUNX1, SCG2, SERINC4, SERPINA1, SIAH2, SKOR2, SPRR4, SVOPL, TCL6, WWOX, ZBED6CL, ZNF75D”

Test set

Full set

Best Hub model (C-Index test)

[INFO] Coefs. list

[1] “ACTC1, ALB, CD8A, CDC42, CDK14, CDK5, CTNNB1, EGFR, EIF5AL1, EPHA3, ERAS, F2, FAU, FEZF2, FLT3, FOS, GAPDH, GNA11, GUCY2D, HRAS, HSP90AA1, JAK2, JUN, KAT2B, LEF1, MAPK1, MAPK11, MGAM, NFKBIA, NOS1, NOS3, NOTCH1, NRAS, PCSK1, PIK3CA, POTEE, PRDM10, PRKG2, RAC1, RAC3, REM2, RPS6KA1, SERPINA1, SRC, TBP, TBPL2, TOP2A, TOP2B, TSPO, TUBB4A, UBC, UBD, UBL4A, UBL4B, WT1, WWOX, YES1”

Test set

Full set

Best Orphan model (C-Index test)

[INFO] Coefs. list

[1] “ENSG00000012171, ENSG00000091583, ENSG00000092199, ENSG00000093167, ENSG00000095932, ENSG00000120256, ENSG00000121871, ENSG00000122375, ENSG00000124343, ENSG00000130720, ENSG00000131080, ENSG00000148426, ENSG00000153485, ENSG00000155008, ENSG00000163166, ENSG00000163202, ENSG00000164744, ENSG00000166509, ENSG00000170270, ENSG00000172667, ENSG00000172967, ENSG00000178522, ENSG00000178997, ENSG00000179363, ENSG00000181977, ENSG00000182759, ENSG00000184716, ENSG00000185028, ENSG00000186075, ENSG00000187082, ENSG00000187416, ENSG00000187754, ENSG00000188735, ENSG00000196406, ENSG00000197584, ENSG00000203661, ENSG00000204450, ENSG00000205517, ENSG00000213578, ENSG00000215474, ENSG00000225880, ENSG00000230445, ENSG00000232948, ENSG00000235453, ENSG00000239887, ENSG00000242473, ENSG00000243284, ENSG00000244057, ENSG00000244694, ENSG00000249581, ENSG00000251493, ENSG00000259288, ENSG00000263201, ENSG00000275163, ENSG00000275553, ENSG00000278599”

Test set

Full set

5.5 Best Log-rank test in all runs

Best Elastic net (Log-rank test)

[INFO] Coefs. list

[1] “ABCB5, AC117457.1, APOH, APOOL, CCDC97, CEL, CLEC4M, CPLX3, ENSG00000281028, EPB41L4B, ERP27, FLT3, GPR152, HNRNPC, IL13RA2, KCNMB2, KIR2DP1, LCE3C, LCE3D, LHFPL3, LHX5, LRP11, MAGEB6B, NFE2, NGB, NOS2, PRAMEF17, PSPC1, PTCHD4, RBMY1E, RELB, RIOX1, RPH3A, SERPINA1, SIAH2, SKOR2, SLC16A2, SLC1A1, SLITRK3, TRIM64, USP17L17, VSIG8, VWC2, YBEY”

Test set

Full set

Best Hub model (Log-rank test)

[INFO] Coefs. list

[1] “ACTC1, ALB, CD8A, CDC42, CDK14, CDK5, CTNNB1, EGFR, EIF5AL1, EPHA3, ERAS, F2, FAU, FEZF2, FLT3, FOS, GAPDH, GNA11, GUCY2D, HRAS, HSP90AA1, JAK2, JUN, KAT2B, LEF1, MAPK1, MAPK11, MGAM, NFKBIA, NOS1, NOS3, NOTCH1, NRAS, PCSK1, PIK3CA, POTEE, PRDM10, PRKG2, RAC1, RAC3, REM2, RPS6KA1, SERPINA1, SRC, TBP, TBPL2, TOP2A, TOP2B, TSPO, TUBB4A, UBC, UBD, UBL4A, UBL4B, WT1, WWOX, YES1”

Test set

Full set

Best Orphan model (Log-rank test)

[INFO] Coefs. list

[1] “AC069503.2, AC117457.1, AMBN, APOH, APOOL, CCDC81, CCDC83, CD1E, CD99L2, CEL, CLEC3A, CLRN2, CPLX3, CXorf49B, CXorf56, DEFB106B, ERICH4, FAM71A, FYB2, GREB1L, H2BU1, HDGFL1, KCNMB2, KIR2DP1, LCE3C, LCE3D, LRP11, LRRFIP2, MAFA, MAGEB6B, NCOR1P1, OR2T5, PTCHD4, PYY3, RIOX1, RPH3A, SERINC4, SKOR2, SLC16A2, SMIM24, SPRR4, STBD1, TBC1D3E, TCL6, TMEM251, ZBED6CL”

Test set

Full set

NULL

6 Parameters for the report

## [INFO]          balanced.sets: TRUE
## [INFO]        calc.params.old: FALSE
## [INFO]           coding.genes: TRUE
## [INFO]     degree.correlation: pearson
## [INFO]          degree.cutoff:       0.000
## [INFO]            degree.type: string
## [INFO]      degree.unweighted: TRUE
## [INFO]      handle.duplicates: keep_first
## [INFO]                   log2: TRUE
## [INFO]                n.cores:      14.000
## [INFO]          normalization: center
## [INFO]                 ntimes:    5000.000
## [INFO]                project: brca.data.2018.09.13
## [INFO]                   seed:    1985.000
## [INFO]                 subset: Inf
## [INFO]   subtract.surv.column: (I do not know how to display this)
## [INFO]            target.vars: list(alpha = 0.2, vars = 39), list(alpha = 0.2, vars = 56), list(alpha = 0.2, vars = 42)
## [INFO]                 tissue: primary.solid.tumor
## [INFO]                  train:       0.800